[Nmrshiftdb-devel] CVS: nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets BackupPortlet.java,1.3,1.4 ResultPortlet.java,1.69,1.70 SubmitPortlet.java,1.87,1.88

[Stefan K. <sh...@us...>]

Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets
In directory usw-pr-cvs1:/tmp/cvs-serv14855/src/java/org/openscience/nmrshiftdb/portlets

Modified Files:
	BackupPortlet.java ResultPortlet.java SubmitPortlet.java 
Log Message:
Changed the serialization back to JSX


Index: BackupPortlet.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/BackupPortlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -r1.3 -r1.4
*** BackupPortlet.java	24 May 2002 12:08:13 -0000	1.3
--- BackupPortlet.java	30 May 2002 15:02:22 -0000	1.4
***************
*** 52,58 ****
  					if(req.getParameter(((File)v.get(i)).getName())!=null){
  						numberOfRestoredFiles++;
! 						FileInputStream in = new FileInputStream((File)v.get(i));
! 						ObjectInputStream s = new ObjectInputStream(in);
! 						AllInOne aio=(AllInOne)s.readObject();
  						aio.saveMe(runData);
  					}
--- 52,57 ----
  					if(req.getParameter(((File)v.get(i)).getName())!=null){
  						numberOfRestoredFiles++;
! 						ObjIn oi=new ObjIn(new FileInputStream((File)v.get(i)));
! 						AllInOne aio=(AllInOne)oi.readObject();
  						aio.saveMe(runData);
  					}

Index: ResultPortlet.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/ResultPortlet.java,v
retrieving revision 1.69
retrieving revision 1.70
diff -C2 -r1.69 -r1.70
*** ResultPortlet.java	30 May 2002 09:48:55 -0000	1.69
--- ResultPortlet.java	30 May 2002 15:02:22 -0000	1.70
***************
*** 242,245 ****
--- 242,248 ----
  				return (new StringElement("Your input did not include a valid signal!"));
  			}
+ 			for(int i=0;i<numberSpectrum.size();i++)
+ 				if(((ValueTriple)numberSpectrum.get(i)).value2>1 || ((ValueTriple)numberSpectrum.get(i)).value2<0)
+ 					return (new StringElement("One of your intensities is more than one or less than zero. Intensities have to be between zero and one!"));
  			SignalComparator sigComp = new SignalComparator();
  			Collections.sort(numberSpectrum, sigComp);

Index: SubmitPortlet.java
===================================================================
RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v
retrieving revision 1.87
retrieving revision 1.88
diff -C2 -r1.87 -r1.88
*** SubmitPortlet.java	29 May 2002 14:11:55 -0000	1.87
--- SubmitPortlet.java	30 May 2002 15:02:22 -0000	1.88
***************
*** 639,642 ****
--- 639,647 ----
  					bondAtoms = DBBondDBAtomPeer.doSelect(critSignals);
  					subData.bondAtoms=bondAtoms;
+ 					//And the names
+ 					Criteria critNames = new Criteria();
+ 					critNames.add(DBChemicalNamePeer.MOLECULE_ID, dbmol.getMoleculeId());
+ 					v=DBChemicalNamePeer.doSelect(critNames);
+ 					subData.chemNames=v;
  				}
  				//Add spectrum to DB
***************
*** 683,715 ****
  				reviewAssignment.setAssignmentDate(now);
  				reviewAssignment.save();
! 				if (nmrprops.getProperty("sendreviewmail").equals("true"))
! 				{
! 					StringBuffer url = javax.servlet.http.HttpUtils.getRequestURL(req);
! 					url.append("pane0/Review?nmrshiftdbaction=reviewbyurl&id=" + spectrum.getSpectrumId() + "&reviewkey=" + spectrum.getReviewKey() + "&userId="+reviewer.getPrimaryKeyAsInt());
! 					MailMessage email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), reviewer.getEmail(), GeneralUtils.getAdminEmail(runData), "Review this input!", "Some input to NMRShiftDB has been assigned to you for review, the id is " + spectrum.getSpectrumId() + ", the URL " + url);
! 					if (email.send() == false)
  					{
! 						Log.error("Sending email to reviewer failed for spectrum " + spectrum.getSpectrumId());
  					}
! 				}
! 				//Create the overall object for serializing
! 				AllInOne aio=new AllInOne(dbmol, spectrum, subData.dbconditions, subData.spectrumConditions, subData.signals, subData.shifts, subData.signalAtoms, dbatoms, bondAtoms, dbbonds, chemNames);
! 				if (nmrprops.getProperty("writeserializedtodir").equals("true")) {
! 					FileOutputStream out = new FileOutputStream(nmrprops.getProperty("serializeddir")+File.separatorChar+now.toString().replace(' ','_')+"_"+time.substring(time.length()-4)+"ms"+".ser");
! 					ObjectOutputStream s = new ObjectOutputStream(out);
! 					s.writeObject(aio);
! 					s.flush();
! 				}
! 				if (nmrprops.getProperty("sendserializedemail").equals("true")) {
! 					ByteArrayOutputStream out = new ByteArrayOutputStream();
! 					ObjectOutputStream s = new ObjectOutputStream(out);
! 					s.writeObject(aio);
! 					s.flush();
! 					MailMessage email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), nmrprops.getProperty("serializedemail"), GeneralUtils.getAdminEmail(runData), "Serialized input from" + now.toString(), out.toString());
! 					if (email.send() == false) {
! 						Log.error("Sending email with serialized input from " + now.toString() +" failed for spectrum " + spectrum.getSpectrumId());
  					}
  				}
- 
  			}
  			catch (Exception ex)
--- 688,718 ----
  				reviewAssignment.setAssignmentDate(now);
  				reviewAssignment.save();
! 				try{
! 					if (nmrprops.getProperty("sendreviewmail").equals("true"))
  					{
! 						StringBuffer url = javax.servlet.http.HttpUtils.getRequestURL(req);
! 						url.append("pane0/Review?nmrshiftdbaction=reviewbyurl&id=" + spectrum.getSpectrumId() + "&reviewkey=" + spectrum.getReviewKey() + "&userId="+reviewer.getPrimaryKeyAsInt());
! 						MailMessage email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), reviewer.getEmail(), GeneralUtils.getAdminEmail(runData), "Review this input!", "Some input to NMRShiftDB has been assigned to you for review, the id is " + spectrum.getSpectrumId() + ", the URL " + url);
! 						if (email.send() == false)
! 						{
! 							Log.error("Sending email to reviewer failed for spectrum " + spectrum.getSpectrumId());
! 						}
  					}
! 					//Create the overall object for serializing
! 					AllInOne aio=new AllInOne(dbmol, spectrum, subData.dbconditions, subData.spectrumConditions, subData.signals, subData.shifts, subData.signalAtoms, dbatoms, bondAtoms, dbbonds, chemNames);
! 					if (nmrprops.getProperty("writeserializedtodir").equals("true")) {
! 						FileWriter out = new FileWriter(nmrprops.getProperty("serializeddir")+File.separatorChar+now.toString().replace(' ','_')+"_"+time.substring(time.length()-4)+"ms"+".ser");
! 						out.write(aio.serializeMe());
! 						out.close();
! 					}
! 					if (nmrprops.getProperty("sendserializedemail").equals("true")) {
! 						MailMessage email = new org.apache.turbine.util.mail.MailMessage(GeneralUtils.getSmtpServer(runData), nmrprops.getProperty("serializedemail"), GeneralUtils.getAdminEmail(runData), "Serialized input from" + now.toString(), aio.serializeMe());
! 						if (email.send() == false) {
! 							Log.error("Sending email with serialized input from " + now.toString() +" failed for spectrum " + spectrum.getSpectrumId());
! 						}
  					}
+ 				}catch(Exception ex){
+ 					Log.error("Error when sending review mail or serializing spectrum  for spectrum " + spectrum.getSpectrumId()+ ": " + ex.getMessage());
  				}
  			}
  			catch (Exception ex)